Amino Acids and Proteins Flashcards
Amino Acids (AA)
Firstly discovered at them beginning of the 19th century.
More than 700 AA in nature but only 22 are building blocks for proteins in cells.
AA: Structure
1) AMINO GROUP
one side of the polypeptide chain in proteins has this group exposed. It is called the N- terminus end.
2) SIDE CHAIN
it defines the chemical characteristics of the amino acid.
3) CARBOXYL GROUP
other side of the polypeptide chain in proteins has this group exposed. It is called the C-terminus end.
Classification of AA:
The chemical characteristics of their side chains
- polar
- non-polar
- charged
- non-charged
- aliphatic
- aromatic
Note:
Y, W and F can also be classified as aromatic because of the aromatic ring they carry.
Classification of AA:
Synthesis
PROTEINOGENIC
are the building blocks of proteins.
20 are encoded by triplets of the genetic code.
2 are incorporated into proteins through specific mechanisms:
- SELENOCYSTEINE
- PYRROLYSINE
They both contain a structural charge in the mRNA sequence allowing a STOP codon not to be recognised as such by a specific tRNA.
NON-PROTOGENIC
can have other biological functions beyond forming proteins:
- GABA
- Carnitine
Are not produced directly and in isolation by standard cellular machinery:
- modified by post-translational modification of the protein in which they are embedded
- occurring post-translationally, once the protein has already formed
- often linked to the function/activity of the protein
Classification of AA:
Essential/Non-essential
1) ESSENTIAL
can’t be synthetized by the body and must be obtaining through the diet.
2) CONDITIONALLY ESSENTIAL
in condition of stress a surplus of these amino acids need to be untaken through the diet to cope with body demand
3) NON ESSENTIAL
can be synthetized by the body
Proteins: Types and Functions
- Actin and Myosin = contractile
- Insulin =
hormonal - Immunoglobulin = protection
- Hemoglobin = transport
- Rubisco = enzyme
- Ferretin = storage
- Spider silk = structural
- Rhodopsin = receptor
The Polypeptide chain
AA are bound together though PEPTIDE BONDS.
A protein is a POLYPEPTIDE chain.
DEHYDRATION SYNTHESIS REACTION
Protein Folding
1) PRIMARY PROTEIN STRUCTURE
is a sequence of a chain of AA
2) SECONDARY PROTEIN STRUCTURE
occurs when the sequence of AA are linked by hydrogen bonds
3) TERTIARY PROTEIN STRUCTURE
occurs when certain attractions are present between alpha helices and pleated sheets
4) QUATERNARY PROTEIN STRUCTURE
is a protein consisting of more than one AA chain.
Alfa-helix
right-hand spiral conformation.
Every backbone NH group donates a hydrogen bind to the backbone C=O group of AA located 3-4 residues earlier along the protein sequence.
It is NOT a hallow structure, it is just a very tight spiral.
Beta-strands/ Beta-sheets
the other common secondary structure is called the beta structure with includes BETA STRANDS and BETA SHEETS
Beta-strands
are portions of the polypeptide chain that are almost fully extended having a zig-zag shape.
They are flexible but not elastic.
Can be on separate polypeptide chains or ion different segments on the same chain.
Can be either PARALLEL or ANTIPARALLEL.
Beta-sheets
Formed by multiple Beta Strands arranged side-by-side.
Beta Sheets are stabilised by hydrogen bonds between carbonyl oxygens and amide hydrogens on adjacent beta strands.
Protein tertiary structure
Overall spatial arrangement of all atoms in a protein.
Stabilised by numerous weak interactions:
- Hydrogen bonds
- Electrostatic and Hydrophobic interactions
- Disulphide bonds
Interacting amino acids are not necessarily next to each other in the primary sequence.
Two classes:
1) fibrous and globular
2) water or lipid-soluble
Alfa-helix and Beta-sheets = 3D structure and interacting together.
Protein quaternary structure
a protein having more than one subunit and sometimes other elements too.
Protein misfolding
mutation in their amino-acid sequence, error in the folding process.
Effects:
- Loss of function
- Gain of function
